Is a "Clone" Really a Clone?

The recent publication of ENCODE's results calls attention to epigenetic factors that may have been overlooked under a more simplistic paradigm of the genome. Cloning through somatic cell nuclear transfer (SCNT) is one such area that is built on the premise that nuclear DNA is the blueprint for the entire organism, and all the information about the organism, including how to make it, is wrapped up in the DNA sequence. SCNT involves removing the nucleus of the organism you want to clone and inserting it into another cell whose nucleus has been removed (usually an oocyte). Through either chemical or electrical stimulation, the cell is "tricked" into thinking that fertilization has occurred and that it should start on the directional process toward becoming an embryo. This is done even though no paternal gametes were used.

There has been some success in cloning animals. Dolly is the most famous cloned animal, but scientists have cloned many other animals including amphibians, dogs, and mice. However, they have found that the SCNT process has a remarkably poor success rate. Even some of these "successful" clones had some developmental and degenerative problems. Dolly, for example, died early, and scientists found that her cells appeared older than her six years. If the cloned cell makes it to the embryo stage, it usually does not survive beyond a few days. So, if all of the A's, T's, G's, and C's are in order, then what is going wrong? A recent paper in Nature may offers some answers.

Cloning is based on a comparatively simplistic view of the genome as well as a simplistic view of development. As it turns out, the paternal gametes are important for producing a viable embryo that will develop into a healthy individual. A new Nature paper reports that some epigenetic factors that are typically passed on in fertilization are not properly passed on in the SCNT process. Specifically, fertilization will rework how much DNA is methylated and where it is methylated, while SCNT does not include this extensive demethylation and methylation process.

"Methyl" is a chemical group (CH3) that attaches to DNA and signals various activities in the cell. Methylation is one of those epigenetic factors that the ENCODE project found within the non-coding regions of DNA. Recent research has shown that improper methylation is implicated in certain diseases and cancers, and is key player in embryonic development as well as stem cell pluriopotency.

In fertilization, the paternal genome will become completely demethylated. The maternal genome remains intact. Chan et al. suppose that this may allow the embryo to begin with an epigenetic "blank slate" where cells can begin to receive those methyl markers that tell them what kind of cells they are going to become. Furthermore, the methyl groups that came from the oocyte serve as signals for various phases and process in development. This process of demethylating the paternal genome is not replicated in the SCNT embryo. For the most part, the embryo has an epigenetic landscape similar to the mature donor cell, rather than a landscape typically seen in a developing zygote. Of the 102 sites examined in the mouse embryos used in the research paper, all lacked the epigenetic information that is usually received from the oocyte and maintained throughout development.

The demethylation process is not an easy one; the researchers cannot just go through and change the methyl groups of their cloned embryo. In an organic chemistry lab, the compounds used to remove a methyl are very strong, and would probably destroy DNA. The body instead uses special proteins to demethylate DNA. Furthermore, demethylation is signaled differently at different regions of the chromosome, meaning that there are different pathways involved.

So, is a clone really a clone? Based on this study, the answer may not be so clear. SCNT is based on a certain view of science that assumes all organisms are built from the bottom up, or from their smallest components. Just put the right chemistry together and you have the organism. Another way to say it is "we are our genes." However, with all of the research coming out about epigenetic factors, perhaps we need to re-think our assumptions. Perhaps constructing an organism is not just matter of transferring DNA, but is actually a very complex, orchestrated process that could only have happened with a specific end goal in mind.